Related to this concept of rectification, there is a "remez" (a hint) in the passuk, "נפשי אויתיך בלילה אף רוחי בקרבי אשחרך." The explanation is that with "my Nefesh," when he merits to completely purify it, until it is able to cling to You (Hashem), with the secret "לדבקה בך," (to cling to him), with this being a yearning and desire, he is "in the night" at the time that he deposits his Nefashot, and they go up [with the secret of Mayin Nukvin" to arouse the "zivug haElyon" (the connection with Hashem).
And from the strength of this desire when he merits and is able to cling to Him there in a complete clinging, he will remain there and not come back down. And when the morning arrives, and the time for the coming down (returning) of the Nefashot, his Nefesh does not come down. Rather, "My Ruach" (his Ruach) comes down, and it enters "into me," in "the morning." Thus, [this requires a better translation,] his Nefesh does not come down, but rather, his Ruach [comes down] and enters into him [so that he can] rectify it, as we described.
Therefore, the Roshei Teivot (first letters of each word of) " 'בלילה 'אף 'רוחי, הוא באר", ("Be'er," or the well), and this is a hint, that when my soul desires you and it elevates to the Be'er haElyon, as we described. But, when a person knows within himself that he has completed his Nefesh, it is appropriate for him to say this passuk, "נפשי אויתיך בלילה וגו'" with all of the kavanah (intention) as we described above.
So that when he sleeps on his bed, through this, he can reach (receive instead) his Ruach, and so to [afterward] his Neshama, and he wouldn't need any more gilgulim [after this]. But understand this hidden secret, *but you must be careful with it* [warning]. The reason for this is that when we say the passuk, "בידך אפקיד רוחי וגו'" we don't mention it [the Nefesh], and our intention is only that our soul should rise in the way of a deposit ONLY.
And it should return and come down [back] to us in the morning. But, the passuk, "נפשי אויתיך" is said [with the intention] that the Nefesh should stay above and that the Ruach or the Neshama should come down [instead of it], as we described above. Shmuel explained the concept of the passuk, "נפשי אויתיך" in Sha'ar 6 of Sha'ar haKavanot, page 131:1.